Package: RChASM
Title: Detection of Chromosomal Aneuploidies in Ancient DNA Studies
Version: 1.0.1
Authors@R: 
    c(
      person(
        given = "Adam B.", 
        family = "Rohrlach",
        email = "adam.rohrlach@adelaide.edu.au", 
        role = c("aut", "cph"),
        comment = c(ORCID = "0000-0002-4204-5018")
      ), 
    person(
      given = "Jono", 
      family = "Tuke", 
      email = "simon.tuke@adelaide.edu.au", 
      role = c("aut", "cre"),
      comment = c(ORCID = "0000-0002-1688-8951")
    ), 
    person(
      given = "Wolfgang", 
      family = "Haak",
      email = "wolfgang_haak@eva.mpg.de", 
      role = "aut",
      comment = c(ORCID = "0000-0003-2475-2007")
    )
    )
Description: An R implementation of ChASM (Chromosomal Aneuploidy
        Screening Methodology): a statistically rigorous Bayesian
        approach for screening data sets for autosomal and sex
        chromosomal aneuploidies. This package takes as input the
        number of (deduplicated) reads mapping to chromosomes 1-22 and
        the X and Y chromosomes, and models these using a
        Dirichlet-multinomial distribution. From this, This package
        returns posterior probabilities of sex chromosomal karyotypes
        (XX, XY, XXY, XYY, XXX and X) and full autosomal aneuploidies
        (trisomy 13, trisomy 18 and trisomy 21). This package also
        returns two diagnostic statistics: (i) a posterior probability
        addressing whether contamination between XX and XY may explain
        the observed sex chromosomal aneuploidy, and (ii) a chi-squared
        statistic measuring whether the observed read counts are too
        divergent from the underlying distribution (and may represent
        abnormal sequencing/quality issues).
License: MIT + file LICENSE
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.3
Imports: checkmate, cowplot, dplyr, EnvStats, ggplot2, ggrepel, ggsci,
        ggstar, magrittr, matrixStats, mclust, rstatix, sirt, stringr,
        tibble, tidyr, readr
LazyData: true
Suggests: knitr, rmarkdown, extraDistr
VignetteBuilder: knitr
Depends: R (>= 3.5.0)
URL: https://jonotuke.github.io/RChASM/,
        https://github.com/jonotuke/RChASM
BugReports: https://github.com/jonotuke/RChASM/issues
Config/pak/sysreqs: libcairo2-dev cmake libfontconfig1-dev
        libfreetype6-dev make libicu-dev libpng-dev libuv1-dev
        libx11-dev
Repository: https://jonotuke.r-universe.dev
Date/Publication: 2026-04-30 20:38:48 UTC
RemoteUrl: https://github.com/jonotuke/rchasm
RemoteRef: HEAD
RemoteSha: 6cf17e35826caaddf2ef62b6f0f16d9cc5966616
NeedsCompilation: no
Packaged: 2026-07-05 06:08:42 UTC; root
Author: Adam B. Rohrlach [aut, cph] (ORCID:
    <https://orcid.org/0000-0002-4204-5018>),
  Jono Tuke [aut, cre] (ORCID: <https://orcid.org/0000-0002-1688-8951>),
  Wolfgang Haak [aut] (ORCID: <https://orcid.org/0000-0003-2475-2007>)
Maintainer: Jono Tuke <simon.tuke@adelaide.edu.au>